Green white peptide algorithm

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This algorithm is used to generate diagrams in GPM display pages that indicate the peptides which are unlikely to be observed in a proteomics experiment. A "green" peptide is unlikely to be observed and all other peptides are "white".

Green/White Peptide Algorithm

For each peptide sequence, if any of the following rules are met, the peptide is rated "green":

  1. the peptide has < 6 residues;
  2. the peptide has > 35 residues;
  3. the peptide has a domain with 7 or more residues in a row exclusively from the list "LIVMACFWY"; or
  4. if the peptide has > 10 residues and > 67% of its residues from the list "LIVMFWY".

All other peptides are "white".

The Perl code that performs this assessment in GPM is the subroutine "unlikely", found in "/thegpm-cgi/".

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